>retro_hsap_4907
ATGAAGGATACAAAAGTATGGATAATAATGGAATATCCTGATGGAGGCTCCACACTAGATCTGTTAGAACCTGGCCCGTT
AGATGAAACCCAGATCATTACTATATTAAGAGAAATACTGAAAGGACTTGATTACCTCCATTCGGAGAAGAAAATCCATA
GAGGTGTTAAAGCGGCCAACGTCCTGCTGTCTGAGCACTGCGAGGTGAAGCTGGTGGACTTTGGCATGGCTGGCCAACTG
GCAGACACCCAGACCAAAAGGAACACTTTTGTGGGCACCCCGTTCTGGATAGCACCCGAGGTCATCAAACAGTCGGCCTA
TGACTCAAAGGCAGACATCTGGTCCCTGGGCATAACAACTATTTAACTTGCAAAAGGAGAACCACCTTATTCCAAGCTGC
ATCCCATGAAAGTTTTATTCCTTATTCCAAAGAACAACCCACCAACGTTGGAAGAAAACTACAGTAAACCCCTCAAGGAG
TTTGTGGAGGCCTGTTTGAATAAAGAGCTGAGCTTTAGACCCACTGCTAAGGAGTTATTGAAGCACAAGTTTATACTACG
CGATACAAAGAAAACTTCCTACTTGACCGAGCTCATCGACAGGTATAAGAGATGGAGGGCAAAGCAGAGCCAAGAAGACT
CGAGCTCCGAGGATTCCAACTCGGAAACAGATGGCCAAGACTCAGTGGGGCAGCGATTCTGGGGACTGGATCTTCACAAT
CCAAGAAAAAGATCCCAAGAATCTTGAGAATGGAGCTCTTCAGCCATCGGATGTAGACAAATAAGATGAAAGACATCCCA
AAGAGGCCTTTCTCTCAGTGTTTATCTACAATTATTTCTCCTCTGCTTGCAGAGTTGAAGAGCCAGGCGTGCGGAGGGAA
CTTGGGGTCCACTGAAGAGCTTCGAGGGGCCATCTACCTGGTGGAGGAGGTGTGCCCCCGCATCTCCGACACCATAGTGG
GCCAGCTCCTGCAGCAGCTCCACAGATATTCTCTAAGTGGTGGAGAAACTTCATCCCAC
ORF - retro_hsap_4907 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
83.43 % |
Parental protein coverage: |
79.35 % |
Number of stop codons detected: |
2 |
Number of frameshifts detected |
2 |
Retrocopy - Parental Gene Alignment:
Parental | LKDTKLWIIMEYLGGGSALDLLEPGPLDETQIATILREILKGLDYLHSEKKIHRDIKAANVLLSEHGEVK |
| .KDTK.WIIMEY..GGS.LDLLEPGPLDETQI.TILREILKGLDYLHSEKKIHR..KAANVLLSEH.EVK |
Retrocopy | MKDTKVWIIMEYPDGGSTLDLLEPGPLDETQIITILREILKGLDYLHSEKKIHRGVKAANVLLSEHCEVK |
|
Parental | LADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGITAIELARGEPPHSELHPMKVLF |
| L.DFG.AGQL.DTQ.KRNTFVGTPFW.APEVIKQSAYDSKADIWSLGIT.I.LA.GEPP.S.LHPMKVLF |
Retrocopy | LVDFGMAGQLADTQTKRNTFVGTPFWIAPEVIKQSAYDSKADIWSLGITTI*LAKGEPPYSKLHPMKVLF |
|
Parental | LIPKNNPPTLEGNYSKPLKEFVEACLNKEPSFRPTAKELLKHKFILRNAKKTSYLTELIDRYKRWKAEQS |
| LIPKNNPPTLE.NYSKPLKEFVEACLNKE.SFRPTAKELLKHKFILR..KKTSYLTELIDRYKRW.A.QS |
Retrocopy | LIPKNNPPTLEENYSKPLKEFVEACLNKELSFRPTAKELLKHKFILRDTKKTSYLTELIDRYKRWRAKQS |
|
Parental | HDDSSSEDSDAETDGQAS-GGSDSGDWIFTIREKDPKNLENGALQPSDLDRNKMKDIPKRPF-SQCLSTI |
| ..DSSSEDS..ETDGQ.S..GSDSGDWIFTI.EKDPKNLENGALQPSD.D.......PK..F.SQCLSTI |
Retrocopy | QEDSSSEDSNSETDGQDS>WGSDSGDWIFTIQEKDPKNLENGALQPSDVDK*DERH-PKEAF>SQCLSTI |
|
Parental | ISPLFAELKEKSQACGGNLGSIEELRGAIYLAEEACPGISDTMVAQLVQRLQRYSLSGGGTSSH |
| ISPL.AEL..KSQACGGNLGS.EELRGAIYL.EE.CP.ISDT.V.QL.Q.L.RYSLSGG.TSSH |
Retrocopy | ISPLLAEL--KSQACGGNLGSTEELRGAIYLVEEVCPRISDTIVGQLLQQLHRYSLSGGETSSH |
|
Legend:
* | Stop codon |
> | Forward frameshift by one nucleotide |
< | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
Library |
Retrocopy expression |
Parental gene expression |
bodymap2_adipose |
0 .30 RPM |
131 .75 RPM |
bodymap2_adrenal |
0 .00 RPM |
101 .06 RPM |
bodymap2_brain |
0 .00 RPM |
82 .72 RPM |
bodymap2_breast |
0 .04 RPM |
91 .79 RPM |
bodymap2_colon |
0 .02 RPM |
174 .06 RPM |
bodymap2_heart |
0 .02 RPM |
82 .48 RPM |
bodymap2_kidney |
0 .00 RPM |
126 .87 RPM |
bodymap2_liver |
0 .00 RPM |
23 .64 RPM |
bodymap2_lung |
0 .00 RPM |
145 .27 RPM |
bodymap2_lymph_node |
0 .00 RPM |
138 .59 RPM |
bodymap2_ovary |
0 .17 RPM |
119 .48 RPM |
bodymap2_prostate |
0 .02 RPM |
218 .32 RPM |
bodymap2_skeletal_muscle |
0 .00 RPM |
73 .77 RPM |
bodymap2_testis |
0 .15 RPM |
168 .85 RPM |
bodymap2_thyroid |
0 .21 RPM |
124 .32 RPM |
bodymap2_white_blood_cells |
0 .00 RPM |
216 .21 RPM |
RNA Polymerase II actvity near the 5' end of retro_hsap_4907 was not detected
No EST(s) were mapped for retro_hsap_4907 retrocopy.
No TSS is located nearby retro_hsap_4907 retrocopy 5' end.
retro_hsap_4907 was not experimentally validated.
Retrocopy orthology:
Retrocopy
retro_hsap_4907 has 3 orthologous retrocopies within
eutheria group
.
Parental genes homology:
Parental genes homology involve
6 parental genes, and
6 retrocopies.
Expression level across human populations :
Library |
Retrogene expression |
CEU_NA11831 |
0 .00 RPM |
CEU_NA11843 |
0 .00 RPM |
CEU_NA11930 |
0 .03 RPM |
CEU_NA12004 |
0 .00 RPM |
CEU_NA12400 |
0 .00 RPM |
CEU_NA12751 |
0 .00 RPM |
CEU_NA12760 |
0 .00 RPM |
CEU_NA12827 |
0 .00 RPM |
CEU_NA12872 |
0 .00 RPM |
CEU_NA12873 |
0 .00 RPM |
FIN_HG00183 |
0 .00 RPM |
FIN_HG00277 |
0 .00 RPM |
FIN_HG00315 |
0 .00 RPM |
FIN_HG00321 |
0 .00 RPM |
FIN_HG00328 |
0 .00 RPM |
FIN_HG00338 |
0 .00 RPM |
FIN_HG00349 |
0 .00 RPM |
FIN_HG00375 |
0 .00 RPM |
FIN_HG00377 |
0 .00 RPM |
FIN_HG00378 |
0 .00 RPM |
GBR_HG00099 |
0 .00 RPM |
GBR_HG00111 |
0 .00 RPM |
GBR_HG00114 |
0 .00 RPM |
GBR_HG00119 |
0 .00 RPM |
GBR_HG00131 |
0 .00 RPM |
GBR_HG00133 |
0 .00 RPM |
GBR_HG00134 |
0 .00 RPM |
GBR_HG00137 |
0 .00 RPM |
GBR_HG00142 |
0 .00 RPM |
GBR_HG00143 |
0 .00 RPM |
TSI_NA20512 |
0 .00 RPM |
TSI_NA20513 |
0 .00 RPM |
TSI_NA20518 |
0 .00 RPM |
TSI_NA20532 |
0 .03 RPM |
TSI_NA20538 |
0 .05 RPM |
TSI_NA20756 |
0 .00 RPM |
TSI_NA20765 |
0 .00 RPM |
TSI_NA20771 |
0 .00 RPM |
TSI_NA20786 |
0 .00 RPM |
TSI_NA20798 |
0 .00 RPM |
YRI_NA18870 |
0 .07 RPM |
YRI_NA18907 |
0 .00 RPM |
YRI_NA18916 |
0 .00 RPM |
YRI_NA19093 |
0 .00 RPM |
YRI_NA19099 |
0 .03 RPM |
YRI_NA19114 |
0 .00 RPM |
YRI_NA19118 |
0 .00 RPM |
YRI_NA19213 |
0 .00 RPM |
YRI_NA19214 |
0 .02 RPM |
YRI_NA19223 |
0 .00 RPM |
Indel association:
No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (
PubMed).